RXP 06 died while running now it wont start

Hi guys
I've a rxp 06 with a few mods (4" Fizzle, Wedge, Ext. Rod, 13/19R,Catch Can)
I was out riding then suddenly then ski died. I tried to start it but it just clicking both in the front and in the engine compartment.
I saw that the ski have take in some water through the intake under the glove-box, so it was a little wet in the front.

A friend towed me into the land, when I picked up the ski on the trailer and move the drain plugs it came pretty much water.

When I came home I started to troubleshoot. I have tested the ski with a new battery, no difference. New startrelay, no difference. Checked all the fuses and they are OK. Checked the oil and it was OK,
I remove the 4" to check the s/c and it was some water in the hose and in the s/c house. I don't know how the water came there.

I removed the sparkplugs and stared to check them, the front and the middle one was OK, but the third was wet. A took a flashlight and looked in the cylinder and it was some kind of gunk there...

I dont know where to start troubleshoot now..

Can the filter leak water into the supercharger?
Can the ski take in water when you're towing (Carbon seal?)